The default setting (set via Unknown context menu) of the Unknown view is to show all characters and words in the current document that you don't know. These are the characters and words for which dictionary entries automatically appear when you're reading. If any character appears in this view that you actually know, just press the spacebar to mark it as Known and have it removed immediately from this view. For recognizable words, similarly press shift-spacebar.
Through the Unknown context menu, you can specify to show all Unknown characters and words for all the documents you've loaded into Chinese Toolbox.